8FX6

Non-ribosomal PCP-C didomain (amide stabilised leucine) acceptor bound state

PDB DOI: https://doi.org/10.2210/pdb8FX6/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Thermobifida fusca YX
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-01-24 Released: 2023-06-21
Deposition Author(s): Ho, Y.T.C., Cryle, M.J.
Funding Organization(s): Australian Research Council (ARC), National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.244
R-Value Work: 0.200
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Not always an innocent bystander: the impact of stabilised phosphopantetheine moieties when studying nonribosomal peptide biosynthesis.

Ho, Y.T.C., Kaczmarski, J.A., Tailhades, J., Izore, T., Steer, D.L., Schittenhelm, R.B., Tosin, M., Jackson, C.J., Cryle, M.J.

(2023) Chem Commun (Camb) 59: 8234-8237

PubMed: 37310188 Search on PubMed
DOI: https://doi.org/10.1039/d3cc01578e
Primary Citation of Related Structures:
8FX6, 8FX7

PubMed Abstract:
Nonribosomal peptide synthetases produce many important peptide natural products and are centred around carrier proteins (CPs) that deliver intermediates to various catalytic domains. We show that the replacement of CP substrate thioesters by stabilised ester analogues leads to active condensation domain complexes, whereas amide stabilisation generates non-functional complexes.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, The Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia. max.cryle@monash.edu.

Macromolecule Content

Total Structure Weight: 114.49 kDa
Atom Count: 8,199
Modelled Residue Count: 1,027
Deposited Residue Count: 1,040
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PCP-C didomain	A, B	520	Thermobifida fusca YX	Mutation(s): 0 Gene Names: Tfu_1867
UniProt
Find proteins for Q47NR9 (Thermobifida fusca (strain YX)) Explore Q47NR9 Go to UniProtKB: Q47NR9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q47NR9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YCK (Subject of Investigation/LOI) Query on YCK Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	N-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]-L-leucinamide C₁₇ H₃₅ N₄ O₈ P OHVFVHYHCFDMRA-JSGCOSHPSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]